A wrapper for running the Semi-Automated Metabolic Map Illustrator (SAMMI) using Python
This package provides a wrapper for running the Semi-Automated Metabolic Map Illustrator (SAMMI) from Python scripts and the Python command line. The SAMMI tool can be found at www.sammitool.com. The package works with the COBRApy toolbox and requires an internet connection to render maps. For more complex, up-to-date examples and to learn how to use the tool please check out the examples in the Jupyter Notebook file.
The SAMMIpy documentation can be found here.
To install the package run
pip install sammi from the Python command line.
To use the SAMMI package run
import sammi from within your python code. The function
sammi.plot reads the template file
index.html located at
sammi.__path__ + '\\browser', and outputs the generated map to the same folder in the file defined within the function (defaulting to
To open previously generated maps use
sammi.openmap(htmlName). Once maps are generated they can be exported in the SAMMI specific format to be shared and saved.
For help check
help(sammi.plot) within Python or read the SAMMIpy documentation here. Users can also look at the examples provided in the documentation and the Jupyter Notebook in this folder. All of the examples provided in the notebook can be run using
n ranges from zero to eleven.